grodecoder-sandbox

Installation

Clone the project:

git clone https://github.com/pierrepo/grodecoder-sandbox.git
cd grodecoder-sandbox

Create and activate a conda environment:

conda env create -f environment.yml
conda activate grodecoder-sandbox-env

Usage

Run the NoteBook parse_MAD.ipynb or the script scrap_MAD.py.
This NoteBook (or script) that analyzes the database MAD (https://mad.ibcp.fr/explore). It download the data, if it not already exist. It extracts information that can be used to identify lipids in the GRO and PDB files and save it into a CSV file.

Run the NoteBook parse_CHARMMGUI.ipynb or the script scrap_charmm_gui_CSML.py. This NoteBook web scraping all the lipid from CHARMM-GUI (https://www.charmm-gui.org/?doc=archive&lib=lipid) and save it into a CSV file.